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FreedomIntelligence/OpenClaw-Medical-SkillsView
Data & Repro
VC
vcf-annotator
Maintainer FreedomIntelligence · Last updated April 1, 2026
Annotate VCF variants with VEP, ClinVar, gnomAD frequencies, and ancestry-aware context. Generates prioritised variant reports.
Original source
FreedomIntelligence/OpenClaw-Medical-Skills
https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/vcf-annotator
- Maintainer
- FreedomIntelligence
- License
- MIT
- Last updated
- April 1, 2026
Skill Snapshot
Key Details From SKILL.md
Key Notes
- You are the VCF Annotator, a specialised agent for variant annotation and interpretation.
- 1. VEP Annotation: Run Ensembl Variant Effect Predictor on VCF files 2. ClinVar Lookup: Cross-reference variants against ClinVar pathogenicity 3. Frequency Context: Add gnomAD population allele frequencies 4. Ancestry-Aware Filtering: Flag variants with population-specific frequency differences 5. Variant Prioritisation: Rank variants by predicted impact (HIGH/MODERATE/LOW/MODIFIER) 6. Report Generation: Markdown report with top variants, population context, and citations.
Source Doc
Excerpt From SKILL.md
Dependencies
vep(Ensembl VEP, local installation with cache)cyvcf2(fast VCF parsing)pandas(data manipulation)- Optional:
bcftools(VCF manipulation)
Example Queries
- "Annotate the variants in patient.vcf with VEP and ClinVar"
- "Find pathogenic variants in this exome VCF"
- "Which variants have different frequencies across populations?"
- "Prioritise the top 20 high-impact variants"
Status
Planned -- implementation targeting Week 2 (Mar 6-12).
Use cases
- Use vcf-annotator in research workflows aligned with this subject area.
- Follow the upstream documentation for the full working procedure.
Not for
- Do not assume this entry replaces the original database documentation or API notes.
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